We investigated butanol recovery by pervaporation separation, using a silicalite-1 membrane, from batch cultures of butanol-producing Clostridium beijerinckii SBP2 grown on sweet sorghum juice as a fermentation medium. The pervaporation system yielded 73% (w/v) butanol from intact feed cultures containing 1% (w/v) butanol, and had a butanol permeation flux of 11 g m−2 h−1. Upon neutralization and activated charcoal treatment of the feed cultures, butanol yield and total flux increased to 82% (w/v) and 40 g m−2 h−1, respectively. This system is applicable to refining processes for practical biobutanol production from a promising energy crop, sweet sorghum.